diff --git a/R/plot_functions.R b/R/plot_functions.R index 54442582..34f9ad49 100644 --- a/R/plot_functions.R +++ b/R/plot_functions.R @@ -2443,7 +2443,7 @@ multitax_bar_pq <- function( summarise(Abundance = sum(Abundance)) %>% filter(Abundance > 0) - psm <- inner_join(psm_2, psm_1[,c("OTU", lvl1, lvl2, lvl3, fact)], + psm <- inner_join(psm_2, psm_1[,c("OTU", lvl1, lvl2, lvl3)], by = join_by("OTU" == "OTU"), multiple = "first") diff --git a/vignettes/tengeler.Rmd b/vignettes/tengeler.Rmd index 57767fa2..5ee04e9e 100644 --- a/vignettes/tengeler.Rmd +++ b/vignettes/tengeler.Rmd @@ -6,6 +6,7 @@ vignette: > %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8} --- + This tutorial explore a phyloseq version of the dataset from Tengeler et al. (2020) available in the `mia` package. ```{r, include = FALSE} @@ -158,6 +159,12 @@ biplot_pq(subset_taxa_pq(ten, taxa_sums(ten) > 3000), multitax_bar_pq(ten, "Phylum", "Class", "Order", "patient_status") ``` + +```{r} +multitax_bar_pq(ten, "Phylum", "Class", "Order", "patient_status", + nb_seq = FALSE, log10trans = FALSE) +``` + # Differential abundance analysis ```{r}